SLC35A1

Summary

SLC35A1 (solute carrier family 35 member A1, HGNC:11021) is a protein-coding gene on chromosome 6q15, encoding CMP-sialic acid transporter (P78382). Transports CMP-sialic acid from the cytosol into the Golgi apparatus, functioning as an antiporter that exchanges CMP-sialic acid for CMP.

The protein encoded by this gene is found in the membrane of the Golgi apparatus, where it transports nucleotide sugars into the Golgi. One such nucleotide sugar is CMP-sialic acid, which is imported into the Golgi by the encoded protein and subsequently glycosylated. Defects in this gene are a cause of congenital disorder of glycosylation type 2F (CDG2F). Two transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 10559 — RefSeq curated summary.

At a glance

• Gene–disease (curated): SLC35A1-congenital disorder of glycosylation (Strong, GenCC)
• GWAS associations: 3
• Clinical variants (ClinVar): 122 total — 2 pathogenic
• Phenotypes (HPO): 39
• Druggable target: yes
• MANE Select transcript: NM_006416

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:11021
Approved symbol	SLC35A1
Name	solute carrier family 35 member A1
Location	6q15
Locus type	gene with protein product
Status	Approved
Aliases	CMPST, hCST, CMP-Sia-Tr
Ensembl gene	ENSG00000164414
Ensembl biotype	protein_coding
OMIM	605634
Entrez	10559

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 12 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000369552, ENST00000369556, ENST00000369557, ENST00000464978, ENST00000894726, ENST00000894727, ENST00000894728, ENST00000894729, ENST00000894730, ENST00000894731, ENST00000913810, ENST00000913811, ENST00000956022

RefSeq mRNA: 2 — MANE Select: NM_006416 NM_001168398, NM_006416

CCDS: CCDS5010, CCDS55043

Canonical transcript exons

ENST00000369552 — 8 exons

Exon	Start	End
ENSE00001835337	87472974	87473019
ENSE00001910371	87511399	87512336
ENSE00003488010	87477362	87477539
ENSE00003502158	87501158	87501310
ENSE00003579515	87500508	87500667
ENSE00003613439	87509041	87509175
ENSE00003614936	87508420	87508596
ENSE00003731152	87506382	87506448

Expression profiles

Bgee: expression breadth ubiquitous, 133 present calls, max score 95.35.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 5.3238 / max 48.7986, expressed in 1567 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
68840	5.3238	1567

Top tissues by expression

134 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
monocyte	CL:0000576	95.35	gold quality
rectum	UBERON:0001052	95.28	gold quality
leukocyte	CL:0000738	95.10	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	94.38	gold quality
right lung	UBERON:0002167	92.60	gold quality
calcaneal tendon	UBERON:0003701	91.35	gold quality
granulocyte	CL:0000094	91.29	gold quality
cerebellar hemisphere	UBERON:0002245	91.24	gold quality
cerebellar cortex	UBERON:0002129	91.20	gold quality
transverse colon	UBERON:0001157	91.19	gold quality
mucosa of transverse colon	UBERON:0004991	91.16	gold quality
endometrium	UBERON:0001295	91.10	gold quality
cerebellum	UBERON:0002037	91.03	gold quality
right adrenal gland cortex	UBERON:0035827	90.84	gold quality
smooth muscle tissue	UBERON:0001135	90.80	gold quality
primary visual cortex	UBERON:0002436	90.61	gold quality
right hemisphere of cerebellum	UBERON:0014890	90.61	gold quality
Brodmann (1909) area 9	UBERON:0013540	90.56	gold quality
right adrenal gland	UBERON:0001233	90.45	gold quality
left adrenal gland	UBERON:0001234	90.27	gold quality
lung	UBERON:0002048	90.26	gold quality
left adrenal gland cortex	UBERON:0035825	90.25	gold quality
saliva-secreting gland	UBERON:0001044	90.23	gold quality
upper lobe of left lung	UBERON:0008952	90.07	gold quality
minor salivary gland	UBERON:0001830	90.00	gold quality
body of uterus	UBERON:0009853	89.99	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	89.84	gold quality
endocervix	UBERON:0000458	89.79	gold quality
adrenal gland	UBERON:0002369	89.72	gold quality
gall bladder	UBERON:0002110	89.68	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	14.07
E-GEOD-124858	no	381.05

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

57 targeting SLC35A1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-8068	99.98	73.85	2376
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-4789-5P	99.98	70.76	2721
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-96-5P	99.95	72.80	2140
HSA-MIR-141-3P	99.94	72.79	2421
HSA-MIR-200A-3P	99.94	72.68	2420
HSA-MIR-9718	99.94	68.91	918
HSA-MIR-3143	99.93	71.96	3104
HSA-MIR-12133	99.92	71.82	2006
HSA-MIR-1271-5P	99.91	71.99	1972
HSA-MIR-137-3P	99.87	74.74	2401
HSA-MIR-3941	99.86	70.54	2735
HSA-MIR-548AZ-5P	99.83	69.94	3230
HSA-MIR-548T-5P	99.83	69.91	3220
HSA-MIR-205-5P	99.81	70.05	1557
HSA-MIR-4719	99.73	72.10	3329
HSA-MIR-561-3P	99.64	70.90	3647
HSA-MIR-5197-5P	99.64	69.08	1494
HSA-MIR-548AV-5P	99.60	70.84	2107
HSA-MIR-548K	99.60	70.84	2107
HSA-MIR-4672	99.50	71.58	2893
HSA-MIR-8054	99.48	70.81	2084
HSA-MIR-12131	99.48	68.72	1673

Literature-anchored findings (GeneRIF, showing 14)

• substrate binding specificity (PMID:12682060)
• this defect is a new type of congenital disorder of glycosylation (CDG) of type IIf affecting the transport of CMP-sialic acid into the Golgi apparatus. (PMID:15576474)
• this study, we introduced two critical genes encoding human CMP-N-acetylneuraminic acid synthetase and CMP-sialic acid transporter into tobacco suspension-cultured cell to pave a route for sialic biosynthetic pathway. (PMID:16343442)
• CMP-sialic acid transporter is localized in the medial-trans Golgi (PMID:16923816)
• We confirm an autosomal recessive, generalized sialylation defect due to mutations in SLC35A1 (PMID:23873973)
• SLC35A1-deficient cells lack of alpha-dystroglycan O-mannosylation, ligand binding and incorporation of sialic acids. (PMID:25552652)
• the SLC35A1 generates additional isoforms through alternative splicing. (PMID:27387429)
• We performed exome sequencing on an individual with a profound neurological presentation and identified rare compound heterozygous mutations, p.Thr156Arg and p.Glu196Lys, in the CMP-sialic acid transporter, SLC35A1. Patient primary fibroblasts and serum showed a considerable decrease in the amount of N- and O-glycans terminating in sialic acid (PMID:28856833)
• Data indicate a congenital deficiency in solute carrier family 35 (CMP-sialic acid transporter), member A1 (SLC35A1) mutation in two siblings born to consanguineous parents and who displayed moderate macrothrombocytopenia. (PMID:30115659)
• Slc35a1 deficiency causes thrombocytopenia due to impaired megakaryocytopoiesis and excessive platelet clearance in the liver. (PMID:32303557)
• Novel Insights into Selected Disease-Causing Mutations within the SLC35A1 Gene Encoding the CMP-Sialic Acid Transporter. (PMID:33396746)
• The promiscuous binding pocket of SLC35A1 ensures redundant transport of CDP-ribitol to the Golgi. (PMID:34015330)
• Knockout of the CMP-Sialic Acid Transporter SLC35A1 in Human Cell Lines Increases Transduction Efficiency of Adeno-Associated Virus 9: Implications for Gene Therapy Potency Assays. (PMID:34069698)
• A three-pocket model for substrate coordination and selectivity by the nucleotide sugar transporters SLC35A1 and SLC35A2. (PMID:34384782)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	slc35a1	ENSDARG00000040180
mus_musculus	Slc35a1	ENSMUSG00000028293
rattus_norvegicus	Slc35a1	ENSRNOG00000008908
caenorhabditis_elegans		WBGENE00022721

Paralogs (4): SLC35A2 (ENSG00000102100), SLC35A3 (ENSG00000117620), SLC35A5 (ENSG00000138459), SLC35A4 (ENSG00000176087)

Protein

Protein identifiers

CMP-sialic acid transporter — P78382 (reviewed: P78382)

Alternative names: Solute carrier family 35 member A1

All UniProt accessions (2): P78382, Q5W1L7

UniProt curated annotations — full annotation on UniProt →

Function. Transports CMP-sialic acid from the cytosol into the Golgi apparatus, functioning as an antiporter that exchanges CMP-sialic acid for CMP. Binds both CMP-sialic acid and free CMP, but has higher affinity for free CMP. Also able to exchange CMP-sialic acid for AMP and UMP. Also mediates the transport of CDP-ribitol.

Subunit / interactions. Monomer.

Subcellular location. Golgi apparatus membrane. Golgi apparatus.

Disease relevance. Congenital disorder of glycosylation 2F (CDG2F) [MIM:603585] CDGs are a family of severe inherited diseases caused by a defect in protein N-glycosylation. They are characterized by under-glycosylated serum proteins. These multisystem disorders present with a wide variety of clinical features, such as disorders of the nervous system development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders, and immunodeficiency. The broad spectrum of features reflects the critical role of N-glycoproteins during embryonic development, differentiation, and maintenance of cell functions. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the nucleotide-sugar transporter family. SLC35A subfamily.

Isoforms (2)

UniProt ID	Names	Canonical?
P78382-1	1	yes
P78382-2	2

RefSeq proteins (2): NP_001161870, NP_006407* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007271	Nuc_sug_transpt	Family
IPR037185	EmrE-like	Homologous_superfamily

Pfam: PF04142

Catalyzed reactions (Rhea), 4 shown:

• CMP-N-acetyl-beta-neuraminate(in) + CMP(out) = CMP-N-acetyl-beta-neuraminate(out) + CMP(in) (RHEA:67724)
• CDP-L-ribitol(in) + CDP(out) = CDP-L-ribitol(out) + CDP(in) (RHEA:71579)
• CMP-N-acetyl-beta-neuraminate(in) + AMP(out) = CMP-N-acetyl-beta-neuraminate(out) + AMP(in) (RHEA:74639)
• UMP(out) + CMP-N-acetyl-beta-neuraminate(in) = UMP(in) + CMP-N-acetyl-beta-neuraminate(out) (RHEA:74643)

UniProt features (33 total): topological domain 11, transmembrane region 10, binding site 6, sequence variant 3, chain 1, region of interest 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P78382-F1	88.26	0.65

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (6): 55; 101–102; 117–124; 188; 210–214; 272

Function

Pathways and Gene Ontology

Reactome pathways

16 pathways

ID	Pathway
R-HSA-4085001	Sialic acid metabolism
R-HSA-5619037	Defective transport by SLC35A1 causes congenital disorder of glycosylation 2F (CDG2F)
R-HSA-5663020	Defective SLC35A1 in sialic acid metabolism causes congenital disorder of glycosylation 2F (CDG2F)
R-HSA-727802	Transport of nucleotide sugars
R-HSA-9939291	Matriglycan biosynthesis on DAG1
R-HSA-1643685	Disease
R-HSA-382551	Transport of small molecules
R-HSA-392499	Metabolism of proteins
R-HSA-425397	Transport of vitamins, nucleosides, and related molecules
R-HSA-425407	SLC-mediated transmembrane transport
R-HSA-446193	Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein
R-HSA-446203	Asparagine N-linked glycosylation
R-HSA-446219	Synthesis of substrates in N-glycan biosythesis
R-HSA-5619102	SLC transporter disorders
R-HSA-5619115	Disorders of transmembrane transporters
R-HSA-597592	Post-translational protein modification

MSigDB gene sets: 428 (showing top): chr6q15, MORF_MTA1, CREL_01, MORF_MBD4, REACTOME_ADAPTIVE_IMMUNE_SYSTEM, PAL_PRMT5_TARGETS_UP, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, GOCC_CELL_SURFACE, GOBP_LEUKOCYTE_MEDIATED_CYTOTOXICITY, GOBP_LEUKOCYTE_MEDIATED_IMMUNITY, GOBP_NUCLEOTIDE_TRANSPORT, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, ATGTTAA_MIR302C, GOBP_ORGANOPHOSPHATE_ESTER_TRANSPORT, GOBP_REGULATION_OF_IMMUNE_RESPONSE

GO Biological Process (7): carbohydrate metabolic process (GO:0005975), N-acetylneuraminate metabolic process (GO:0006054), CMP-N-acetylneuraminate biosynthetic process (GO:0006055), protein O-linked glycosylation (GO:0006493), CMP-N-acetylneuraminate transmembrane transport (GO:0015782), protein modification process (GO:0036211), pyrimidine nucleotide-sugar transmembrane transport (GO:0090481)

GO Molecular Function (5): CMP-N-acetylneuraminate transmembrane transporter activity (GO:0005456), pyrimidine nucleotide transmembrane transporter activity (GO:0015218), antiporter activity (GO:0015297), protein binding (GO:0005515), pyrimidine nucleotide-sugar transmembrane transporter activity (GO:0015165)

GO Cellular Component (4): Golgi membrane (GO:0000139), Golgi apparatus (GO:0005794), plasma membrane (GO:0005886), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-12 pathways:

Category	Pathways
SLC transporter disorders	2
Synthesis of substrates in N-glycan biosythesis	1
Transport of vitamins, nucleosides, and related molecules	1
DAG1 glycosylations	1
SLC-mediated transmembrane transport	1
Transport of small molecules	1
Asparagine N-linked glycosylation	1
Post-translational protein modification	1
Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein	1
Disorders of transmembrane transporters	1
Disease	1
Metabolism of proteins	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
pyrimidine nucleotide-sugar transmembrane transport	2
primary metabolic process	1
amino sugar metabolic process	1
carboxylic acid metabolic process	1
nucleotide-sugar biosynthetic process	1
CMP-N-acetylneuraminate metabolic process	1
glycoprotein biosynthetic process	1
protein metabolic process	1
macromolecule modification	1
nucleotide-sugar transmembrane transport	1
pyrimidine nucleotide-sugar transmembrane transporter activity	1
CMP-N-acetylneuraminate transmembrane transport	1
pyrimidine nucleotide transport	1
nucleotide transmembrane transporter activity	1
secondary active transmembrane transporter activity	1
binding	1
nucleotide-sugar transmembrane transporter activity	1
Golgi apparatus	1
bounding membrane of organelle	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1
membrane	1
cell periphery	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1290 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SLC35A1	ADGRL1	O94910	969
SLC35A1	SLC35D2	Q76EJ3	929
SLC35A1	SLC35D1	Q9NTN3	928
SLC35A1	SLC35D3	Q5M8T2	920
SLC35A1	GNE	Q9Y223	761
SLC35A1	SLC35C1	Q96A29	746
SLC35A1	PMM2	O15305	741
SLC35A1	NANS	Q9NR45	715
SLC35A1	CMAS	Q8NFW8	703
SLC35A1	ST3GAL5	Q9UNP4	623
SLC35A1	SLC35E1	Q96K37	619
SLC35A1	ST3GAL4	Q11206	600
SLC35A1	SLC35B4	Q969S0	566
SLC35A1	SLC35B3	Q9H1N7	564
SLC35A1	ST6GALNAC1	Q9NSC7	563

IntAct

109 interactions, top by confidence:

A	B	Type	Score
SLC35A1	LHFPL5	psi-mi:“MI:0915”(physical association)	0.560
SLC35A1	KIR3DL3	psi-mi:“MI:0915”(physical association)	0.560
SLC35A1		psi-mi:“MI:0915”(physical association)	0.560
SLC35A1	MCFD2	psi-mi:“MI:0915”(physical association)	0.560
SLC35A1	CD53	psi-mi:“MI:0915”(physical association)	0.560
SLC35A1	SLC34A2	psi-mi:“MI:0915”(physical association)	0.560
SLC35A1	TMX2	psi-mi:“MI:0915”(physical association)	0.560
SLC35A1	SLC1A1	psi-mi:“MI:0915”(physical association)	0.560
TMPRSS2	SLC35A1	psi-mi:“MI:0915”(physical association)	0.560
SLC35A1	BCL2L13	psi-mi:“MI:0915”(physical association)	0.560
SLC35A1	ASZ1	psi-mi:“MI:0915”(physical association)	0.560
SLC35A1	PLPP4	psi-mi:“MI:0915”(physical association)	0.560
ASGR2	SLC35A1	psi-mi:“MI:0915”(physical association)	0.560
SDC3	SLC35A1	psi-mi:“MI:0915”(physical association)	0.560
SLC35A1	ERGIC3	psi-mi:“MI:0915”(physical association)	0.560
SLC35A1	F11R	psi-mi:“MI:0915”(physical association)	0.560
SLC35A1	FXYD3	psi-mi:“MI:0915”(physical association)	0.560
SLC35A1	RELL2	psi-mi:“MI:0915”(physical association)	0.560
SLC35A1	PIK3IP1	psi-mi:“MI:0915”(physical association)	0.560
TCTA	SLC35A1	psi-mi:“MI:0915”(physical association)	0.560
SLC35A1	FNDC9	psi-mi:“MI:0915”(physical association)	0.560
SLC35A1	CERS4	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (78): ACBD3 (Affinity Capture-MS), SLC35A1 (Synthetic Lethality), ICK (Affinity Capture-MS), CASP3 (Affinity Capture-MS), SLC35A1 (Two-hybrid), SLC35A1 (Negative Genetic), SLC35A1 (Negative Genetic), SLC35A1 (Negative Genetic), SLC35A1 (Positive Genetic), SLC35A1 (Negative Genetic), SLC35A1 (Negative Genetic), SLC35A1 (Negative Genetic), SLC35A1 (Negative Genetic), SLC35A1 (Positive Genetic), SLC35A1 (Negative Genetic)

ESM2 similar proteins: A4IFK2, A4IHW3, A7S1L6, A9UUB8, O08520, O16658, O77592, P78381, P78382, P78383, P87041, P97858, Q02334, Q18779, Q1JQ66, Q29Q28, Q3E6T0, Q55DM5, Q58DA6, Q61420, Q66HX0, Q6AXR5, Q6GQ70, Q6PGC7, Q6V7K3, Q6YC49, Q753T9, Q7Z769, Q8AWB6, Q8AXS6, Q8MII5, Q8MXJ9, Q8R1T4, Q8WMS0, Q93890, Q94EI9, Q95YI5, Q968A5, Q9C8M1, Q9LFN3

Diamond homologs: A0JMG9, A4IHW3, B8B7Q4, O16658, O77592, P78381, P78382, Q01IU9, Q02334, Q05B73, Q58DA6, Q5RA79, Q61420, Q654D9, Q6AXR5, Q6K8S7, Q6YC49, Q6ZL17, Q7X7C4, Q8GY97, Q8LGE9, Q8MIA3, Q8R1T4, Q8WMS0, Q91ZR7, Q96G79, Q9C5H6, Q9D321, Q9R0M8, Q9Y2D2, B8B350, F4JN00, O08520, P87041, B8A7Q8, Q5N855, Q93890, Q09875, Q5R4D7, Q8LES0

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
SLC35A1	“up-regulates quantity”	“sialic acid”	relocalization

Disease & clinical

Clinical variants and AI predictions

ClinVar

122 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	2
Likely pathogenic	0
Uncertain significance	44
Likely benign	48
Benign	18

Top pathogenic / likely-pathogenic (2)

Variant ID	HGVS	Classification
1703752	NM_006416.5(SLC35A1):c.439T>C (p.Ser147Pro)	Pathogenic
488412	NM_006416.5(SLC35A1):c.303G>C (p.Gln101His)	Pathogenic

SpliceAI

2328 predictions. Top by Δscore:

Variant	Effect	Δscore
19:35903347:ACAGT:A	acceptor_gain	1.0000
19:35903348:CAG:C	acceptor_loss	1.0000
19:35903349:A:AG	acceptor_gain	1.0000
19:35903349:A:G	acceptor_loss	1.0000
19:35903349:AGT:A	acceptor_gain	1.0000
19:35903350:G:GA	acceptor_gain	1.0000
19:35903350:GT:G	acceptor_gain	1.0000
19:35903350:GTG:G	acceptor_gain	1.0000
6:87477484:GCC:G	donor_gain	1.0000
6:87477499:G:GT	donor_gain	1.0000
6:87500505:A:G	acceptor_gain	1.0000
6:87501153:TTTA:T	acceptor_loss	1.0000
6:87501156:A:AG	acceptor_gain	1.0000
6:87501156:A:G	acceptor_loss	1.0000
6:87501156:AG:A	acceptor_gain	1.0000
6:87501156:AGGT:A	acceptor_gain	1.0000
6:87501157:G:GA	acceptor_gain	1.0000
6:87501157:GG:G	acceptor_gain	1.0000
6:87501157:GGT:G	acceptor_gain	1.0000
6:87501157:GGTG:G	acceptor_gain	1.0000
6:87501308:GTG:G	donor_gain	1.0000
6:87501308:GTGGT:G	donor_loss	1.0000
6:87501310:GGTA:G	donor_loss	1.0000
6:87501311:GTAAG:G	donor_loss	1.0000
6:87501312:T:A	donor_loss	1.0000
6:87508419:GGA:G	acceptor_gain	1.0000
6:87508597:G:GG	donor_gain	1.0000
6:87509035:T:G	acceptor_gain	1.0000
6:87509038:A:AG	acceptor_gain	1.0000
6:87509039:A:AG	acceptor_gain	1.0000

AlphaMissense

2132 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:87477510:G:C	K55N	0.999
6:87477510:G:T	K55N	0.999
6:87501189:C:A	A129D	0.999
6:87508432:A:T	E196V	0.999
6:87509049:A:C	S254R	0.999
6:87509051:T:A	S254R	0.999
6:87509051:T:G	S254R	0.999
6:87509105:A:C	K272N	0.999
6:87509105:A:T	K272N	0.999
6:87477508:A:G	K55E	0.998
6:87477520:A:C	S59R	0.998
6:87477522:T:A	S59R	0.998
6:87477522:T:G	S59R	0.998
6:87500648:T:C	L112P	0.998
6:87501182:T:C	C127R	0.998
6:87501194:T:C	C131R	0.998
6:87501263:G:A	G154R	0.998
6:87501263:G:C	G154R	0.998
6:87501264:G:A	G154E	0.998
6:87506433:T:C	C187R	0.998
6:87506440:G:A	G189E	0.998
6:87508464:T:A	W207R	0.998
6:87508464:T:C	W207R	0.998
6:87509096:C:A	N269K	0.998
6:87509096:C:G	N269K	0.998
6:87511416:G:C	G302R	0.998
6:87500587:A:C	S92R	0.997
6:87500589:T:A	S92R	0.997
6:87500589:T:G	S92R	0.997
6:87500605:T:C	Y98H	0.997

dbSNP variants (sampled 300 via entrez): RS1000047863 (6:87476682 G>A), RS1000136125 (6:87510139 T>A,C), RS1000329126 (6:87502258 T>C), RS1000501538 (6:87495551 C>T), RS1000524981 (6:87479872 A>AC), RS1000591971 (6:87509207 T>C), RS1000737800 (6:87488937 C>T), RS1000769041 (6:87488552 A>G), RS1000917983 (6:87511238 T>C), RS1000922309 (6:87481741 A>G), RS1001020136 (6:87495280 C>A), RS1001049041 (6:87475169 A>G), RS1001054098 (6:87494063 A>T), RS1001070451 (6:87492297 T>C,G), RS1001189981 (6:87480467 A>G)

Disease associations

OMIM: gene MIM:605634 | disease phenotypes: MIM:603585

GenCC curated gene-disease

Disease	Classification	Inheritance
SLC35A1-congenital disorder of glycosylation	Strong	Autosomal recessive

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

Disease	Classification	Inheritance
SLC35A1-congenital disorder of glycosylation	Moderate	AR

Mondo (1): SLC35A1-congenital disorder of glycosylation (MONDO:0011342)

Orphanet (1): SLC35A1-CDG (Orphanet:238459)

HPO phenotypes

39 total (30 of 39 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0000093	Proteinuria
HP:0000252	Microcephaly
HP:0000322	Short philtrum
HP:0000465	Webbed neck
HP:0000490	Deeply set eye
HP:0000601	Hypotelorism
HP:0000639	Nystagmus
HP:0001249	Intellectual disability
HP:0001250	Seizure
HP:0001251	Ataxia
HP:0001260	Dysarthria
HP:0001263	Global developmental delay
HP:0001265	Hyporeflexia
HP:0001290	Generalized hypotonia
HP:0001298	Encephalopathy
HP:0001659	Aortic regurgitation
HP:0001873	Thrombocytopenia
HP:0001875	Decreased total neutrophil count
HP:0001892	Abnormal bleeding
HP:0001902	Giant platelets
HP:0001933	Subcutaneous hemorrhage
HP:0002090	Pneumonia
HP:0002098	Respiratory distress
HP:0002310	Orofacial dyskinesia
HP:0002465	Poor speech
HP:0002718	Recurrent bacterial infections
HP:0003010	Prolonged bleeding time
HP:0003355	Aminoaciduria
HP:0003593	Infantile onset

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST001762_245	Obesity-related traits	4.000000e-06
GCST001762_760	Obesity-related traits	4.000000e-06
GCST006444_24	Bone mineral density (hip)	9.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0005106	body composition measurement
EFO:0007702	hip bone mineral density

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C567040	Congenital Disorder Of Glycosylation, Type IIF (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6067234 (SINGLE PROTEIN)

PharmGKB: 1 entry (VIP=true, CPIC=false)

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: transporter — SLC35 family of nucleotide sugar transporters

ChEMBL bioactivities

2 potent at pChembl≥5 of 2 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
5.40	Kd	4018	nM	CHEMBL5653589
5.40	ED50	4018	nM	CHEMBL5653589

PubChem BioAssay actives

1 with measured affinity, of 2 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide	2149418: Binding affinity to human SLC35A1 incubated for 45 mins by Kinobead based pull down assay	kd	4.0184	uM

CTD chemical–gene interactions

41 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Particulate Matter	increases abundance, affects cotreatment, decreases reaction, increases expression, decreases expression	3
Air Pollutants	affects cotreatment, increases abundance, increases oxidation, decreases expression	2
Arsenic	decreases methylation, increases abundance, decreases expression	2
Valproic Acid	affects expression, decreases methylation	2
dicrotophos	decreases expression	1
triphenyl phosphate	affects expression	1
alpha-pinene	affects cotreatment, increases oxidation, increases abundance	1
bisphenol A	decreases expression	1
sodium arsenite	increases abundance, decreases expression	1
potassium chromate(VI)	decreases expression, affects cotreatment	1
methacrylaldehyde	affects cotreatment, increases oxidation, increases abundance	1
beta-methylcholine	affects expression	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
di-n-butylphosphoric acid	affects expression	1
abrine	decreases expression	1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amide	decreases reaction, increases expression	1
jinfukang	decreases expression	1
Decitabine	affects expression	1
Acrolein	affects cotreatment, increases oxidation, increases abundance	1
Air Pollutants, Occupational	decreases expression	1
Ethanol	decreases expression, increases abundance, affects cotreatment	1
Vehicle Emissions	decreases reaction, increases expression	1
Cisplatin	affects expression	1
Estradiol	decreases expression	1
Gasoline	affects cotreatment, decreases expression, increases abundance	1
Methyl Methanesulfonate	increases expression	1
Nickel	decreases expression	1
Nicotine	increases expression	1
Ozone	affects cotreatment, increases oxidation, increases abundance	1
Phthalic Acids	decreases methylation	1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5652460	Binding	Binding affinity to human SLC35A1 incubated for 45 mins by Kinobead based pull down assay	NVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

Cellosaurus cell lines

12 cell lines: 8 cancer cell line, 3 transformed cell line, 1 spontaneously immortalized cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_B2FX	Abcam HeLa SLC35A1 KO	Cancer cell line	Female
CVCL_C3MF	SfSWT-6	Spontaneously immortalized cell line	Female
CVCL_DX37	HAP1 GAN (-) SLC35A1 (-) 1	Cancer cell line	Male
CVCL_DX38	HAP1 GAN (-) SLC35A1 (-) 2	Cancer cell line	Male
CVCL_DX39	HAP1 GAN (-) SLC35A1 (-) 3	Cancer cell line	Male
CVCL_DX40	HAP1 GAN (-) SLC35A1 (-) 4	Cancer cell line	Male
CVCL_E2QG	HEK293T SLC35A1 KO	Transformed cell line	Female
CVCL_E2QH	HEK293T AGA/SLC35A1 DKO	Transformed cell line	Female
CVCL_E2QI	HeLa SLC35A1 KO	Cancer cell line	Female
CVCL_RN08	PDIS-22	Transformed cell line	Female

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.